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Sample GSM7113417 Query DataSets for GSM7113417
Status Public on Sep 22, 2023
Title TSC1
Sample type SRA
 
Source name Prostate
Organism Homo sapiens
Characteristics tissue: Prostate
cell type: primary tissue slice
sample type: primary tissue slice
genotype: WT
treatment: tissue slice culture in PrEBM for two days
Treatment protocol Prostate tissue slices, epithelial cells, and stromal cells were grown to 70% confluence and then cultured in EV-free media for two days. Evs were isolated from the cell media by differential ultracentifugation.
Growth protocol Patient-derived prostate epithelial cells were maintained in PrEBM media in humidified atmosphere with 5% CO2 at 37C. Patient-derived prostate stromal cells were maintained in MCDB media with 5% FBS and DHT and Fgfb in humidified atmosphere with 5% CO2 at 37C. Patient-derived prostate tissue slices were maintained in PrEBM media in humidified atmosphere with 5% CO2 at 37C.
Extracted molecule total RNA
Extraction protocol Primary epithelial cell, stromal cell, and tissue slice RNA was harvested using miRNeasy Mini kit (Qiagen). Primary epithelial cell EV, stromal cell EV, tissue slice EV, and serum EV RNA was harvested using the Serum/Plasma miRNeasy kit (Qiagen). 100 ng of total RNA was used for the construction of cell and tissue sequencing libraries. 5 uL of RNA was used for the construction of cell EV, tissue EV, and serum EV sequencing libraries.
microRNA libraries for smallRNA-seq were prepared using the QIAseq miRNA Library Kit following manufacturer's protocols. Libraries were diluted to 10 nM for sequencing.
smallRNA-seq by HiSeq 4000 single read 100 nucleotides
 
Library strategy miRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 4000
 
Description TSC3_pz_Day_0_ATCACG
primary sequencing analysis (mapping) TISSUE_CELLS.xlsx
non_ev_CPM_tmm_normalizedcounts_no_piR.xlsx
Data processing GeneGlobe data analysis center
Reads were trimmed using cutadapt, which removed the 3' adapters and low-quality bases
MicroRNA sequences with less than 16 bp and UMI sequences less than 10 bp were removed
MicroRNAs were mapped to miRBase using bowtie, which allowed up to two mismatches
Assembly: miRBase version 22
Supplementary files format and content: Excel files (CPM_tmm_normalizedcounts)
 
Submission date Mar 23, 2023
Last update date Sep 22, 2023
Contact name Morgan Zenner
E-mail(s) zenner2@uic.edu
Phone 8473728777
Organization name University of Illinois at Chicago College of Medicine
Department Pathology
Lab Larisa Nonn
Street address 909 South Wolcott Ave
City Chicago
State/province IL
ZIP/Postal code 60612
Country USA
 
Platform ID GPL20301
Series (1)
GSE228062 Prostate tissue explant, epithelial cell, stromal cell, and extracellular vesicle microRNA characterization by NGS
Relations
BioSample SAMN33872765
SRA SRX19758304

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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